- Browse accessible chromatin region of the biosample
| Sample ID: |
Sample_0639 |
| Biosample name: |
TFAP2C knockout line 2 UCLA hESCs cultured for 5 days |
| Biosample type: |
Stem Cell |
| Tissue type: |
Embryo |
| Cancer type: |
Normal |
| Region number: |
21676 |
| Length: |
11064.906 kb |
| GEO/SRA ID: |
SRR5815115 |
| Mean insert size: |
229.264 |
| Standard deviation: |
204.843 |
| TSS enrichment score: |
8.40126 |
| FRiP: |
0.06479 |
|
Diasgnostic plot |
The percentages of read pairs in FR,
RF, and TANDEM orientations.
|
TF footprint of TFAP2C knockout line 2 UCLA hESCs cultured for 5 days
Peak annotation visualization of
TFAP2C knockout line 2 UCLA hESCs cultured for 5 days
| Plot A: a pie chart of annotated genomic features. |
| Note A: the proportion of annotating genomic region (Promoter, 5'UTR, 3'UTR, Exon, Intron, Downstream and Intergenic). |
| Plot B: a heatmap of peaks binding to TSS region. |
| Note B: the profile of ATAC peaks binding to TSS region (+/- 1kb). |
Software and parameters used
| Read mapping: |
bowtie2(v2.2.5) -p 10 -X 2000 -x -S |
| Duplicates Removing: |
picard MarkDuplicates REMOVE_DUPLICATES=true ASSUME_SORTED=true |
| Peak calling: |
macs2(2.1.2) --broad--SPMR --nomodel --extsize 200 -q 0.01 |
| Trimming the adapter: |
trim_galore --phred33 --stringency 3 --length 20 |
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